8F1J: SigN RNA polymerase early-melted intermediate
SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A). Determined by electron microscopy at 2.6 Å resolution. Released 5 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 2.6 Å
- Organisms
- Aquifex aeolicus, Escherichia coli
- Chains
- 10
- Atoms
- 30,829
- Mol. weight
- 491.11 kDa
- Ligands
- ZN, MG
- Released
- 5 Apr 2023
Explore 8F1J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8F1J contains 185 α-helices and 219 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain G: 6 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-20 | 9 | 1 |
| β-strand | 23-31 | 9 | 1 |
| α-helix | 35-49 | 15 | |
| β-strand | 52-61 | 10 | 2 |
| β-strand | 74 | 1 | 3 |
| α-helix | 78-86 | 9 | |
| β-strand | 90-92 | 3 | 4 |
| β-strand | 97-105 | 9 | 2 |
| β-strand | 108-111 | 4 | 3 |
| α-helix | 112-114 | 3 | |
| β-strand | 115 | 1 | 2 |
| α-helix | 116-117 | 2 | |
| β-strand | 121-123 | 3 | 4 |
| β-strand | 129-133 | 5 | 3 |
| β-strand | 139-150 | 12 | 2 |
| β-strand | 152-153 | 2 | 5 |
| α-helix | 166-167 | 2 | |
| β-strand | 170-172 | 3 | 2 |
| β-strand | 175-176 | 2 | 5 |
| β-strand | 180-189 | 10 | 1 |
| β-strand | 199-207 | 9 | 1 |
| α-helix | 213-233 | 21 | |
Chain H: 11 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15-18 | 4 | 6 |
| β-strand | 23-31 | 9 | 6 |
| α-helix | 35-49 | 15 | |
| β-strand | 52-61 | 10 | 7 |
| β-strand | 74 | 1 | 8 |
| α-helix | 78-86 | 9 | |
| β-strand | 90-92 | 3 | 9 |
| β-strand | 97-105 | 9 | 7 |
| β-strand | 108-111 | 4 | 8 |
| α-helix | 112-114 | 3 | |
| α-helix | 116-117 | 2 | |
| β-strand | 121-123 | 3 | 9 |
| β-strand | 129-133 | 5 | 8 |
| β-strand | 139-150 | 12 | 7 |
| β-strand | 152-153 | 2 | 10 |
| β-strand | 170-172 | 3 | 7 |
| β-strand | 175-176 | 2 | 10 |
| β-strand | 180-190 | 11 | 6 |
| β-strand | 198-207 | 10 | 6 |
| α-helix | 213-226 | 14 | |
| α-helix | 251-254 | 4 | |
| β-strand | 256 | 1 | 11 |
| α-helix | 257-259 | 3 | |
| α-helix | 264-272 | 9 | |
| β-strand | 277 | 1 | 11 |
| α-helix | 278-282 | 5 | |
| α-helix | 286-290 | 5 | |
| α-helix | 297-308 | 12 | |
Chain I: 66 helices, 92 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| α-helix | 11-12 | 2 | |
| β-strand | 13-14 | 2 | 12 |
| α-helix | 19-20 | 2 | |
| α-helix | 29-39 | 11 | |
| α-helix | 49-56 | 8 | |
| β-strand | 59-60 | 2 | 13 |
| β-strand | 66-75 | 10 | 13 |
| α-helix | 76-78 | 3 | |
| α-helix | 82-88 | 7 | |
| β-strand | 93-104 | 12 | 13 |
| β-strand | 116-128 | 13 | 13 |
| β-strand | 136-137 | 2 | 14 |
| β-strand | 142-145 | 4 | 14 |
| α-helix | 146 | 1 | |
| β-strand | 147-151 | 5 | 15 |
| α-helix | 152 | 1 | |
| β-strand | 154-160 | 7 | 16 |
| β-strand | 171-177 | 7 | 16 |
| β-strand | 180 | 1 | 17 |
| β-strand | 184-187 | 4 | 16 |
| β-strand | 195-198 | 4 | 16 |
| β-strand | 204-205 | 2 | 16 |
| α-helix | 206-212 | 7 | |
| α-helix | 217-224 | 8 | |
| β-strand | 227-231 | 5 | 18 |
| β-strand | 239-240 | 2 | 18 |
| α-helix | 243-246 | 4 | |
| β-strand | 250 | 1 | 19 |
| β-strand | 255-257 | 3 | 20 |
| β-strand | 260-263 | 4 | 20 |
| α-helix | 267 | 1 | |
| β-strand | 268 | 1 | 19 |
| α-helix | 269 | 1 | |
| α-helix | 271-280 | 10 | |
| β-strand | 284-285 | 2 | 18 |
| α-helix | 289-292 | 4 | |
| β-strand | 296-297 | 2 | 18 |
| β-strand | 301-302 | 2 | 21 |
| β-strand | 309-311 | 3 | 21 |
| β-strand | 315-316 | 2 | 18 |
| α-helix | 319-326 | 8 | |
| β-strand | 332-336 | 5 | 18 |
| α-helix | 347-353 | 7 | |
| α-helix | 360-370 | 11 | |
| α-helix | 378-389 | 12 | |
| β-strand | 396 | 1 | 17 |
| α-helix | 399-408 | 10 | |
| α-helix | 422-437 | 16 | |
| β-strand | 451-454 | 4 | 15 |
| α-helix | 456-478 | 23 | |
| α-helix | 489-492 | 4 | |
| α-helix | 496-508 | 13 | |
| β-strand | 512-514 | 3 | 14 |
| α-helix | 515-516 | 2 | |
| α-helix | 520-527 | 8 | |
| β-strand | 529-531 | 3 | 15 |
| α-helix | 546-548 | 3 | |
| α-helix | 550-551 | 2 | |
| α-helix | 552-554 | 3 | |
| β-strand | 558 | 1 | 22 |
| β-strand | 572-574 | 3 | 15 |
| β-strand | 575 | 1 | 22 |
| β-strand | 576 | 1 | 23 |
| β-strand | 580-581 | 2 | 24 |
| β-strand | 587-595 | 9 | 24 |
| β-strand | 598-607 | 10 | 24 |
| α-helix | 608-611 | 4 | |
| β-strand | 616-617 | 2 | 24 |
| β-strand | 628 | 1 | 24 |
| β-strand | 634-637 | 4 | 24 |
| β-strand | 642-645 | 4 | 24 |
| α-helix | 647-649 | 3 | |
| β-strand | 652-654 | 3 | 24 |
| β-strand | 662 | 1 | 23 |
| α-helix | 665-667 | 3 | |
| α-helix | 671-673 | 3 | |
| α-helix | 676-686 | 11 | |
| β-strand | 689 | 1 | 25 |
| α-helix | 690-691 | 2 | |
| β-strand | 701 | 1 | 12 |
| α-helix | 705-711 | 7 | |
| β-strand | 716-717 | 2 | 26 |
| β-strand | 722-727 | 6 | 27 |
| β-strand | 731-736 | 6 | 27 |
| α-helix | 738-740 | 3 | |
| α-helix | 741-742 | 2 | |
| β-strand | 748-752 | 5 | 27 |
| α-helix | 753-754 | 2 | |
| β-strand | 757-758 | 2 | 28 |
| β-strand | 763 | 1 | 29 |
| β-strand | 764-765 | 2 | 28 |
| β-strand | 768-769 | 2 | 26 |
| β-strand | 776-777 | 2 | 27 |
| β-strand | 782-785 | 4 | 26 |
| β-strand | 789-790 | 2 | 30 |
| β-strand | 793-794 | 2 | 30 |
| β-strand | 798-804 | 7 | 31 |
| β-strand | 815-819 | 5 | 31 |
| α-helix | 820-824 | 5 | |
| β-strand | 830-841 | 12 | 29 |
| β-strand | 842 | 1 | 32 |
| β-strand | 847 | 1 | 32 |
| β-strand | 849-850 | 2 | 33 |
| α-helix | 860-862 | 3 | |
| β-strand | 865 | 1 | 34 |
| β-strand | 870 | 1 | 35 |
| β-strand | 871 | 1 | 34 |
| α-helix | 872 | 1 | |
| β-strand | 876-877 | 2 | 29 |
| β-strand | 882-884 | 3 | 35 |
| β-strand | 886-887 | 2 | 33 |
| α-helix | 897-906 | 10 | |
| β-strand | 918-919 | 2 | 35 |
| α-helix | 920-921 | 2 | |
| β-strand | 926-935 | 10 | 29 |
| β-strand | 936 | 1 | 36 |
| α-helix | 940-941 | 2 | |
| α-helix | 943-979 | 37 | |
| α-helix | 988-991 | 4 | |
| α-helix | 1011-1037 | 27 | |
| β-strand | 1040 | 1 | 36 |
| β-strand | 1046-1058 | 13 | 29 |
| α-helix | 1059-1060 | 2 | |
| β-strand | 1065-1067 | 3 | 31 |
| β-strand | 1073-1080 | 8 | 31 |
| α-helix | 1082-1084 | 3 | |
| β-strand | 1087 | 1 | 37 |
| α-helix | 1092 | 1 | |
| β-strand | 1093 | 1 | 37 |
| α-helix | 1094 | 1 | |
| β-strand | 1096-1098 | 3 | 31 |
| α-helix | 1102-1106 | 5 | |
| α-helix | 1110-1133 | 24 | |
| α-helix | 1138-1150 | 13 | |
| α-helix | 1161-1163 | 3 | |
| α-helix | 1166-1175 | 10 | |
| β-strand | 1182-1183 | 2 | 12 |
| α-helix | 1192-1201 | 10 | |
| β-strand | 1209-1210 | 2 | 38 |
| β-strand | 1213 | 1 | 37 |
| α-helix | 1219 | 1 | |
| β-strand | 1220 | 1 | 37 |
| α-helix | 1221 | 1 | |
| β-strand | 1225-1226 | 2 | 38 |
| β-strand | 1227-1234 | 8 | 31 |
| β-strand | 1235 | 1 | 25 |
| α-helix | 1239-1241 | 3 | |
| β-strand | 1244-1246 | 3 | 39 |
| β-strand | 1251 | 1 | 40 |
| β-strand | 1252 | 1 | 41 |
| β-strand | 1258 | 1 | 40 |
| β-strand | 1268-1270 | 3 | 42 |
| α-helix | 1272-1281 | 10 | |
| α-helix | 1284-1291 | 8 | |
| α-helix | 1298-1309 | 12 | |
| α-helix | 1321-1331 | 11 | |
| β-strand | 1335-1340 | 6 | 43 |
Chain J: 75 helices, 79 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| β-strand | 19-24 | 6 | 43 |
| α-helix | 25-26 | 2 | |
| α-helix | 27-33 | 7 | |
| β-strand | 34-37 | 4 | 44 |
| β-strand | 44 | 1 | 45 |
| β-strand | 51 | 1 | 45 |
| α-helix | 52 | 1 | |
| α-helix | 59-62 | 4 | |
| α-helix | 78-80 | 3 | |
| α-helix | 83 | 1 | |
| β-strand | 84 | 1 | 46 |
| α-helix | 85 | 1 | |
| β-strand | 91 | 1 | 46 |
| α-helix | 95-99 | 5 | |
| β-strand | 102-112 | 11 | 44 |
| α-helix | 115-118 | 4 | |
| α-helix | 123-128 | 6 | |
| α-helix | 132-139 | 8 | |
| β-strand | 144-148 | 5 | 47 |
| β-strand | 159-160 | 2 | 47 |
| α-helix | 162-172 | 11 | |
| β-strand | 177-179 | 3 | 47 |
| α-helix | 182-190 | 9 | |
| α-helix | 194-207 | 14 | |
| α-helix | 212-229 | 18 | |
| α-helix | 234-237 | 4 | |
| β-strand | 238-244 | 7 | 44 |
| α-helix | 247-249 | 3 | |
| α-helix | 256-258 | 3 | |
| α-helix | 264-284 | 21 | |
| α-helix | 289-307 | 19 | |
| β-strand | 317 | 1 | 48 |
| β-strand | 323 | 1 | 48 |
| α-helix | 324-325 | 2 | |
| α-helix | 327-331 | 5 | |
| α-helix | 337 | 1 | |
| α-helix | 338-342 | 5 | |
| β-strand | 345-347 | 3 | 42 |
| β-strand | 350-354 | 5 | 39 |
| β-strand | 355-357 | 3 | 49 |
| β-strand | 365-369 | 5 | 49 |
| α-helix | 370-376 | 7 | |
| α-helix | 378-387 | 10 | |
| α-helix | 394-403 | 10 | |
| α-helix | 406-415 | 10 | |
| β-strand | 421-424 | 4 | 39 |
| α-helix | 431-433 | 3 | |
| β-strand | 434-437 | 4 | 39 |
| β-strand | 438-442 | 5 | 49 |
| β-strand | 447-449 | 3 | 49 |
| α-helix | 451-453 | 3 | |
| α-helix | 454-457 | 4 | |
| β-strand | 465-469 | 5 | 39 |
| α-helix | 474-482 | 9 | |
| β-strand | 485 | 1 | 39 |
| α-helix | 486-488 | 3 | |
| β-strand | 491 | 1 | 50 |
| β-strand | 498 | 1 | 50 |
| α-helix | 505-513 | 9 | |
| β-strand | 526-527 | 2 | 51 |
| α-helix | 530-538 | 9 | |
| β-strand | 547-557 | 11 | 51 |
| β-strand | 563-573 | 11 | 51 |
| α-helix | 574-580 | 7 | |
| α-helix | 589-591 | 3 | |
| α-helix | 598-611 | 14 | |
| α-helix | 615-635 | 21 | |
| α-helix | 641-643 | 3 | |
| α-helix | 645-647 | 3 | |
| α-helix | 650-669 | 20 | |
| α-helix | 675-701 | 27 | |
| β-strand | 703-707 | 5 | 52 |
| β-strand | 713-717 | 5 | 52 |
| α-helix | 721-727 | 7 | |
| α-helix | 734-741 | 8 | |
| β-strand | 745 | 1 | 53 |
| β-strand | 748 | 1 | 54 |
| α-helix | 753 | 1 | |
| β-strand | 754 | 1 | 54 |
| α-helix | 755 | 1 | |
| β-strand | 759 | 1 | 53 |
| α-helix | 766-767 | 2 | |
| α-helix | 769-803 | 35 | |
| β-strand | 809-811 | 3 | 55 |
| β-strand | 820-822 | 3 | 56 |
| β-strand | 825-827 | 3 | 57 |
| β-strand | 830-833 | 4 | 57 |
| α-helix | 836-839 | 4 | |
| β-strand | 843 | 1 | 58 |
| β-strand | 844 | 1 | 56 |
| α-helix | 847 | 1 | |
| β-strand | 848-849 | 2 | 59 |
| α-helix | 850 | 1 | |
| β-strand | 856-858 | 3 | 59 |
| β-strand | 863 | 1 | 58 |
| α-helix | 866-874 | 9 | |
| β-strand | 880-882 | 3 | 56 |
| β-strand | 894-895 | 2 | 55 |
| α-helix | 896-899 | 4 | |
| β-strand | 901 | 1 | 60 |
| β-strand | 908 | 1 | 60 |
| α-helix | 909-910 | 2 | |
| α-helix | 915-924 | 10 | |
| α-helix | 925-929 | 5 | |
| β-strand | 949-951 | 3 | 61 |
| β-strand | 956-961 | 6 | 62 |
| β-strand | 965-967 | 3 | 61 |
| β-strand | 973-975 | 3 | 61 |
| β-strand | 981-985 | 5 | 62 |
| β-strand | 991-996 | 6 | 62 |
| α-helix | 997-998 | 2 | |
| β-strand | 1002-1003 | 2 | 61 |
| β-strand | 1010-1011 | 2 | 62 |
| β-strand | 1016-1019 | 4 | 61 |
| β-strand | 1034-1038 | 5 | 63 |
| β-strand | 1042 | 1 | 64 |
| β-strand | 1046-1048 | 3 | 64 |
| β-strand | 1059-1061 | 3 | 64 |
| α-helix | 1070-1073 | 4 | |
| β-strand | 1077-1081 | 5 | 63 |
| β-strand | 1087 | 1 | 63 |
| β-strand | 1089 | 1 | 65 |
| α-helix | 1090 | 1 | |
| β-strand | 1096 | 1 | 65 |
| β-strand | 1098-1100 | 3 | 63 |
| β-strand | 1105-1107 | 3 | 64 |
| β-strand | 1122-1123 | 2 | 64 |
| α-helix | 1138-1146 | 9 | |
| α-helix | 1148-1150 | 3 | |
| α-helix | 1153-1155 | 3 | |
| β-strand | 1156 | 1 | 66 |
| β-strand | 1161-1165 | 5 | 67 |
| β-strand | 1170 | 1 | 68 |
| β-strand | 1172 | 1 | 68 |
| β-strand | 1174-1178 | 5 | 67 |
| β-strand | 1187-1189 | 3 | 67 |
| β-strand | 1203-1204 | 2 | 67 |
| β-strand | 1209 | 1 | 66 |
| α-helix | 1214-1216 | 3 | |
| α-helix | 1217-1224 | 8 | |
| α-helix | 1226-1242 | 17 | |
| α-helix | 1250-1260 | 11 | |
| β-strand | 1263-1268 | 6 | 69 |
| β-strand | 1279-1281 | 3 | 69 |
| α-helix | 1282-1293 | 12 | |
| β-strand | 1301-1305 | 5 | 69 |
| α-helix | 1309-1313 | 5 | |
| α-helix | 1319-1325 | 7 | |
| α-helix | 1328-1338 | 11 | |
| β-strand | 1341-1342 | 2 | 43 |
| α-helix | 1347-1352 | 6 | |
| α-helix | 1360-1362 | 3 | |
| α-helix | 1363-1372 | 10 | |
Chain K: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| α-helix | 16-31 | 16 | |
| α-helix | 35-37 | 3 | |
| α-helix | 46-55 | 10 | |
| α-helix | 61-79 | 19 | |
Chain M: 22 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-24 | 6 | |
| α-helix | 30-41 | 12 | |
| β-strand | 47-48 | 2 | 70 |
| β-strand | 115 | 1 | 41 |
| α-helix | 116-118 | 3 | |
| α-helix | 120-129 | 10 | |
| α-helix | 135-146 | 12 | |
| β-strand | 148 | 1 | 71 |
| β-strand | 153 | 1 | 72 |
| β-strand | 154 | 1 | 71 |
| α-helix | 158-165 | 8 | |
| α-helix | 172-182 | 11 | |
| β-strand | 192 | 1 | 72 |
| α-helix | 195-203 | 9 | |
| α-helix | 213-222 | 10 | |
| α-helix | 225-228 | 4 | |
| α-helix | 234-239 | 6 | |
| α-helix | 243-254 | 12 | |
| α-helix | 260-262 | 3 | |
| β-strand | 276-281 | 6 | 73 |
| β-strand | 284-289 | 6 | 73 |
| β-strand | 298-299 | 2 | 70 |
| α-helix | 301-304 | 4 | |
| α-helix | 313-350 | 38 | |
| α-helix | 353-357 | 5 | |
| β-strand | 365 | 1 | 74 |
| α-helix | 367-373 | 7 | |
| α-helix | 378-384 | 7 | |
| β-strand | 390-392 | 3 | 73 |
| β-strand | 395-397 | 3 | 73 |
| β-strand | 403 | 1 | 74 |
| β-strand | 406-407 | 2 | 75 |
| β-strand | 415-416 | 2 | 75 |
| α-helix | 417-429 | 13 | |
| α-helix | 439-446 | 8 | |
| α-helix | 455-464 | 10 | |
| α-helix | 470-472 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (36-mer) | A, C | DNA | 36 | Aquifex aeolicus | |
| DNA-directed RNA polymerase subunit alpha | G, H | protein | 329 | Escherichia coli | P0A7Z4 (AlphaFold model) |
| DNA-directed RNA polymerase subunit beta | I | protein | 1342 | Escherichia coli | P0A8V2 (AlphaFold model) |
| DNA-directed RNA polymerase subunit beta' | J | protein | 1430 | Escherichia coli | P0A8T7 (AlphaFold model) |
| DNA-directed RNA polymerase subunit omega | K | protein | 91 | Escherichia coli | P0A800 (AlphaFold model) |
| RNA polymerase sigma-54 factor | M | protein | 480 | Escherichia coli | P24255 |
| DNA (36-mer) | B, D | DNA | 36 | Aquifex aeolicus | |
Sequence of entity 1 (A, C), FASTA
>8F1J_1 DNA (36-MER) (chains A, C)
CCAGAAATTGGCACGAAAATTGCCTTAAATACAACG
Sequence of entity 2 (G, H), FASTA
>8F1J_2 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 3 (I), FASTA
>8F1J_3 DNA-directed RNA polymerase subunit beta (chains I)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE
Sequence of entity 4 (J), FASTA
>8F1J_4 DNA-directed RNA polymerase subunit beta' (chains J)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH
Sequence of entity 5 (K), FASTA
>8F1J_5 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 6 (M), FASTA
>8F1J_6 RNA polymerase sigma-54 factor (chains M)
SEFMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEID
TRETQDSETLDTADALEQKEMPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETT
QTLQDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEIDIDEVEA
VLKRIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMR
VTRLKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRL
QINQHYASMCNNARNDGDSQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQ
GEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASS
TAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV
Sequence of entity 7 (B, D), FASTA
>8F1J_7 DNA (36-MER) (chains B, D)
CGTTGTATTTATAGCAATTTTCGTGCCAATTTCTGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 1 |
Primary citation
A general mechanism for transcription bubble nucleation in bacteria. Mueller, A.U., Chen, J., Wu, M. et al. Proc Natl Acad Sci U S A (2023) 120:e2220874120-e2220874120. DOI 10.1073/pnas.2220874120 · PubMed
Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3K4G 2.05 Å, Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
- 8FVW 2.1 Å, CryoEM structure of E.coli transcription elongation complex bound to ppGpp
- 8FVR 2.42 Å, CryoEM structure of E.coli transcription elongation complex
- 9ZP4 2.42 Å, E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a…
- 8HKC 2.49 Å, Cryo-EM structure of E. coli RNAP sigma32 complex
- 1BDF 2.5 Å, Structure of escherichia coli RNA polymerase alpha subunit N-terminal domain
- 6XL5 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
- 6XL9 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA…
- 12EC 2.6 Å, Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC…
- 8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
- 9MSF 2.6 Å, de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic…
- 9YMV 2.6 Å, De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product…
Browse structure collections
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